---
session_id: "session_20260502_r7t4w9"
branch: "feat/domain-knot-libraries"
created_at: "2026-05-02T00:00:00Z"
current_mode: "code"
version: "1.0"
---

## Session Overview

**Branch:** feat/domain-knot-libraries
**Started:** 2026-05-02 UTC
**Current Mode:** code
**Status:** Phase 4 Round 3 COMPLETE — 33 formats shipped + cleanup done. Pending: Block 9 docs.

## Mode History

| Mode | Entered | Exited | Summary |
|------|---------|--------|---------|
| plan | 2026-04-29 | 2026-04-29 | Designed domain knot libraries PRD/ARD for DE/Agents/ML/Health/Signal/OilGas |
| code | 2026-04-30 | 2026-04-30 | Phase 1–3: Package infra, Connectors (priority + extended tiers), Data domain (Tier 1/2/3/4, specializations, validation) — 811 tests |
| code | 2026-05-01 | 2026-05-01 | Phase 4 Rounds 1+2: 64 file formats across 10 waves (universal tabular, codecs, lakehouse, scientific tabular, documents, genomics, geospatial, ML artifacts, images) — 3261 tests |
| code | 2026-05-02 | - | Phase 4 Round 3: DICOM test + remaining 33 formats (B2/B3/B5/C1/C2/E waves) |

## Actions Taken

### 2026-04-29 — plan mode
- Designed domain-knot-libraries PRD and ARD
- Established block structure: Blocks 2–9 (connectors, data, agents, ml, health, signal, oilgas, docs)
- Created execution-plan.md

### 2026-04-30 — code mode
- Phase 1 (commit ae90db3): Package infra, connectors priority tier (sqlite/duckdb/postgres/local/s3/kafka/valkey), Layer 1+2 knots, KnotResolver, sweet_tea registry
- Phase 3 review: security/perf fixes, Layer 1+2 conventions refactor (one class per file, interfaces not Protocols, no free functions, SOLID)
- Phase 4 foundation (commit ae90db3): FileFormat hierarchy, FileSource/FileSink knots, LakehouseTable interface + knots

### 2026-05-01 — code mode
- Phase 4 Round 1 (commit 86436b2): Wave A1 (11 universal tabular), Wave A4 (5 compression codecs), Wave A3 (3 lakehouse) — 226 tests
- Phase 4 Round 2 (commit 4b2bdbd): Wave A2 (6 scientific), Wave B1 (8 documents), Wave B4 (7 genomics), Wave C3 (5 geospatial), Wave D1 (7 ML artifacts), Wave D2 (5 images) — 456 tests
- Suite: 3261 passing, 6 skipped, 0 failing
- B3 agent hit rate limit after writing dicom_format.py (287 lines, untracked, no test)
- Security review completed: planning/current/security-review-2026-05-01.md
- Phase 4 progress tracker: planning/current/phase4-progress.md

### 2026-05-02 — code mode
- Updated session file to reflect full Phase 4 history
- Wave B3 DICOM: wrote test_dicom_format.py (36 tests); committed dicom_format.py + test (57d0220)
- Wave C1 Audio: wav/flac/ogg/mp3/aac/m4a — 24 pass, 3 skip (pydub/py3.13 pyaudioop removed)
- Wave C2 Oil&Gas: segy/las/dlis/witsml/prodml/resqml/segd — 32 pass, 4 skip; committed (e37519f)
- Wave E Specialty: fits/asdf/netcdf4/root/grib — 9 pass, 4 skip; committed (e37519f)
- Wave B2 Healthcare clinical: fhir_json/fhir_xml/hl7v2/cda_xml/define_xml/sdtm_xpt — 56 pass, 2 skip
- Wave B3 Remaining: nifti/bids_dataset/open_slide/mzml — 31 pass
- Wave B5 Healthcare biosignal: edf/edf_plus/bdf/brainvision — 49 pass; committed (51d7f43)
- Cleanup B4a: moved free functions in fastq/vcf/bcf into class @staticmethods
- Archive: implemented ArchiveFileFormat tar/zip/tar.gz/tar.bz2/tar.zst read+write
- Committed cleanup + archive (4b5635a)
- Full suite: 3507 passed, 19 skipped, 0 failed

## Context Summary

**Where we are:** Phase 4 Round 3 COMPLETE. All formats shipped. Suite at 3507 passing, 19 skipped, 0 failed.

**Commits this session:**
- 57d0220 — Wave B3 DICOM (36 tests)
- e37519f — Waves C1/C2/E (74 tests)
- 51d7f43 — Waves B2/B3-remaining/B5 (136 tests)
- 4b5635a — Cleanup B4a + ArchiveFileFormat

**What's left:**
- Block 9: Documentation & Polish (per-domain docs, connector matrix, contributing guide, README, CHANGELOG, mkdocs nav)
- Epub/hdf5 test verification (low priority — agent flagged possible flakes; suite currently shows 0 failures)

### 2026-05-06 — document mode (doc audit, round 1)
- Audited all 22 docs files listed in Block 9 task
- Fixed docs/architecture.md: SubscribableStore row — PostgresStore and ValKeyStore changed from "Planned" to "Y"; mid-run extension text updated to reflect all three implementations
- Fixed docs/domains/health.md: removed `ClinicalDataQualityGate` backward-compat alias reference (Gate→Check remediation)
- Fixed docs/guides/testing.md: Knot subclass unit test pattern updated to instantiate inside `with Tapestry():` block (new required test pattern)
- All other files in scope confirmed accurate

### 2026-05-06 — document mode (doc audit, round 2 — post-knot-remediation)
- Audited 13 target docs for knot design rules accuracy (no __init__ validation, no self._x in Knot __init__, no __new__ bypass, no *Gate quality knot names, no Math: N/A)
- docs/guides/testing.md: working-tree fix already applied (with Tapestry(): pattern), confirmed correct
- All 13 files confirmed accurate; no additional changes required

### 2026-05-06 — code mode (ruff remediation)
- Fixed all remaining ruff errors across pirn/domains/ and tests/unit/domains/
- B905: added strict=False to 17 zip() calls (agents, connectors, ml, data tests)
- RUF002/RUF003: replaced EN DASH/MULTIPLICATION SIGN/MINUS SIGN in 50+ source files (oilgas, signal, ml, health, connectors)
- RUF005: replaced list/tuple concatenation with iterable unpacking in 9 files (oilgas/well, ml/features, agents/rag, ablation)
- RUF015: replaced list()[0] with next(iter()) in cosmosdb_pool, firestore_pool
- RUF059: prefixed unused unpacked vars with _ in flac_format, grib_format, mzml_format
- RUF046: removed redundant int() wrapper in epoch_extractor
- F841: removed unused local vars (n_channels, config, rt_unit) in brainvision/kinesis/mzml
- B007: renamed unused loop vars to _ prefix (confusion_matrix_analyzer, ablation, mzml)
- B017: changed assertRaises(Exception) to specific types in 5 test files
- F401: fixed eland import pattern in test_eland_source/to_pandas
- F821: fixed _Builder forward-reference in test_delta_table
- E741: renamed l to up in rational_resampler_pipeline
- I001: fixed import ordering in 7 ray test files (pytest before pirn locals)
- Final: ruff check passes clean (All checks passed!)

### 2026-05-06 — code mode
- Step11 compliance: added TestProcess classes to 26 agents domain knot test files
- New files: test_llm_provider_knot.py, test_memory_store_knot.py
- Modified 24 existing test files across rag/, reflection/, specialized_agents/, structured_output/, tool_use/, document_processing/
- Updated knot-violations-audit-agents-2026-05-06.md: all 26 Step11 [ ] → [x], Step12 updated accordingly
- Updated knot-violations-audit-aggregate-2026-05-06.md: agents Step11/Step12 → 0, TOTAL 113→87

**Key patterns:**
- `BatchFileFormat` subclass with `_decode_full` / `_encode_full`
- `StreamingFileFormat` for line-oriented text formats
- `pytest.importorskip("package")` at top of test files for optional deps
- PHI-bearing formats (DICOM, FHIR, HL7v2): hash/strip PII in decode path
- FormatRoundTrip helper in `tests/unit/domains/connectors/file_formats/_format_round_trip.py`
- ClassVar convention: lower_snake names (no UPPER_SNAKE)
- No module-level free functions — wrap in class staticmethods

**Next steps:**
1. Write DICOM test → commit dicom_format.py + test
2. Dispatch parallel agents for remaining waves
3. Cleanup pass (B4a, batch 1 backlog items)
4. Block 9 docs

## Notes
- B4a convention violation flagged in phase4-progress.md: fasta/fastq/vcf/bcf have module-level helpers. Cleanup tracked in execution-plan.md Batch 1.
- GeoPackage tests: 7 tests skip on Python 3.14 (no fiona wheels) — expected, not a failure.
- Ray Data tests quarantined under tests/slow/ — excluded from default run.
- sweet_tea upstream issue: KnotResolver 3 xfail tests pending upstream fix.
